Dataset for 'Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model'

SARS-CoV-2’s transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. Primarily, the dataset contains (1) fastq files from next-generation sequencing of a small amplicon that contains the barcode of our barcoded viruses and (2) associated count matrices showing how many of each barcode are present in each sample. Secondarily, RT-qPCR results measuring viral titers in various respiratory tissues are also included.

严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）的传播瓶颈至今仍未得到充分表征，部分原因在于缺乏定量测量工具。为解决这一问题，我们改造了SARS-CoV-2反向遗传系统，以生成包含超过200株同基因SARS-CoV-2病毒的库，这些病毒在非翻译开放阅读框ORF10（Open Reading Frame 10）中插入了特定的6核苷酸条形码（barcode）。我们经鼻内途径将此带条形码的病毒库直接接种于供体叙利亚金黄仓鼠，随后让配对的未接触过病毒的接触仓鼠分别与每只供体仓鼠接触。暴露后，我们采集了鼻甲、气管和肺组织，测定了病毒滴度，并对每个组织中的条形码数量进行计数，以量化传播瓶颈。本研究调整了暴露时长与暴露途径（经空气传播、直接接触及污染物接触），以评估其对传播瓶颈的影响。本数据集主要包含两部分内容：(1) 针对携带条形码的小扩增子进行下一代测序（Next-Generation Sequencing, NGS）得到的FASTQ文件；(2) 用于展示每个样本中各类条形码对应数量的关联计数矩阵。此外，本数据集还附带了用于测定各类呼吸道组织病毒滴度的逆转录定量聚合酶链反应（Reverse Transcription Quantitative Polymerase Chain Reaction, RT-qPCR）结果。